// clang-format off
/* -*- c++ -*- ----------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://www.lammps.org/, Sandia National Laboratories
   LAMMPS development team: developers@lammps.org

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

#include "npair_multi_old.h"

#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "molecule.h"
#include "my_page.h"
#include "neigh_list.h"

#include <cmath>

using namespace LAMMPS_NS;

/* ---------------------------------------------------------------------- */

template<int HALF, int NEWTON, int TRI, int SIZE>
NPairMultiOld<HALF, NEWTON, TRI, SIZE>::NPairMultiOld(LAMMPS *lmp) : NPair(lmp) {}

/* ----------------------------------------------------------------------
  multi/old-type stencil is itype dependent and is distance checked
  Full:
    binned neighbor list construction for all neighbors
    multi-type stencil is itype dependent and is distance checked
    every neighbor pair appears in list of both atoms i and j
  Half + newtoff:
    binned neighbor list construction with partial Newton's 3rd law
    each owned atom i checks own bin and other bins in stencil
    multi-type stencil is itype dependent and is distance checked
    pair stored once if i,j are both owned and i < j
    pair stored by me if j is ghost (also stored by proc owning j)
  Half + newton:
    binned neighbor list construction with full Newton's 3rd law
    each owned atom i checks its own bin and other bins in Newton stencil
    multi-type stencil is itype dependent and is distance checked
    every pair stored exactly once by some processor
------------------------------------------------------------------------- */

template<int HALF, int NEWTON, int TRI, int SIZE>
void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
{
  int i, j, jh, k, n, itype, jtype, ibin, bin_start, which, ns, imol, iatom, moltemplate;
  tagint itag, jtag, tagprev;
  double xtmp, ytmp, ztmp, delx, dely, delz, rsq, radsum, cut, cutsq;
  int *neighptr, *s;
  double *cutnsq, *distsq;

  const double delta = 0.01 * force->angstrom;

  double **x = atom->x;
  double *radius = atom->radius;
  int *type = atom->type;
  int *mask = atom->mask;
  tagint *tag = atom->tag;
  tagint *molecule = atom->molecule;
  tagint **special = atom->special;
  int **nspecial = atom->nspecial;
  int nlocal = atom->nlocal;
  if (includegroup) nlocal = atom->nfirst;

  int *molindex = atom->molindex;
  int *molatom = atom->molatom;
  Molecule **onemols = atom->avec->onemols;
  if (molecular == Atom::TEMPLATE)
    moltemplate = 1;
  else
    moltemplate = 0;

  int history = list->history;
  int mask_history = 1 << HISTBITS;

  int *ilist = list->ilist;
  int *numneigh = list->numneigh;
  int **firstneigh = list->firstneigh;
  MyPage<int> *ipage = list->ipage;

  int inum = 0;
  ipage->reset();

  for (i = 0; i < nlocal; i++) {
    n = 0;
    neighptr = ipage->vget();

    itag = tag[i];
    itype = type[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    if (moltemplate) {
      imol = molindex[i];
      iatom = molatom[i];
      tagprev = tag[i] - iatom - 1;
    }

    ibin = atom2bin[i];
    s = stencil_multi_old[itype];
    distsq = distsq_multi_old[itype];
    cutnsq = cutneighsq[itype];
    ns = nstencil_multi_old[itype];
    for (k = 0; k < ns; k++) {
      bin_start = binhead[ibin + s[k]];
      if (HALF && NEWTON && (!TRI)) {
        if (k == 0) {
          // Half neighbor list, newton on, orthonormal
          // loop over rest of atoms in i's bin, ghosts are at end of linked list
          bin_start = bins[i];
        }
      }

      for (j = bin_start; j >= 0; j = bins[j]) {
        if (!HALF) {
          // Full neighbor list
          // only skip i = j
          if (i == j) continue;
        } else if (!NEWTON) {
          // Half neighbor list, newton off
          // only store pair if i < j
          // stores own/own pairs only once
          // stores own/ghost pairs on both procs
          if (j <= i) continue;
        } else if (TRI) {
          // Half neighbor list, newton on, triclinic
          // for triclinic, bin stencil is full in all 3 dims
          // must use itag/jtag to eliminate half the I/J interactions
          // cannot use I/J exact coord comparision
          //   b/c transforming orthog -> lambda -> orthog for ghost atoms
          //   with an added PBC offset can shift all 3 coords by epsilon
          if (j <= i) continue;
          if (j >= nlocal) {
            jtag = tag[j];
            if (itag > jtag) {
              if ((itag + jtag) % 2 == 0) continue;
            } else if (itag < jtag) {
              if ((itag + jtag) % 2 == 1) continue;
            } else {
              if (fabs(x[j][2] - ztmp) > delta) {
                if (x[j][2] < ztmp) continue;
              } else if (fabs(x[j][1] - ytmp) > delta) {
                if (x[j][1] < ytmp) continue;
              } else {
                if (x[j][0] < xtmp) continue;
              }
            }
          }
        } else {
          // Half neighbor list, newton on, orthonormal
          // store every pair for every bin in stencil,except for i's bin

          if (k == 0) {
            // if j is owned atom, store it, since j is beyond i in linked list
            // if j is ghost, only store if j coords are "above and to the "right" of i
            if (j >= nlocal) {
              if (x[j][2] < ztmp) continue;
              if (x[j][2] == ztmp) {
                if (x[j][1] < ytmp) continue;
                if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
              }
            }
          }
        }

        jtype = type[j];
        if (cutnsq[jtype] < distsq[k]) continue;

        if (exclude && exclusion(i, j, itype, jtype, mask, molecule)) continue;

        delx = xtmp - x[j][0];
        dely = ytmp - x[j][1];
        delz = ztmp - x[j][2];
        rsq = delx * delx + dely * dely + delz * delz;

        if (SIZE) {
          radsum = radius[i] + radius[j];
          cut = radsum + skin;
          cutsq = cut * cut;

          if (rsq <= cutsq) {
            jh = j;
            if (history && rsq < radsum * radsum)
              jh = jh ^ mask_history;

            if (molecular != Atom::ATOMIC) {
              if (!moltemplate)
                which = find_special(special[i], nspecial[i], tag[j]);
              else if (imol >= 0)
                which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
                                     tag[j] - tagprev);
              else
                which = 0;
              if (which == 0)
                neighptr[n++] = jh;
              else if (domain->minimum_image_check(delx, dely, delz))
                neighptr[n++] = jh;
              else if (which > 0)
                neighptr[n++] = jh ^ (which << SBBITS);
            } else
              neighptr[n++] = jh;
          }
        } else {
          if (rsq <= cutneighsq[itype][jtype]) {
            if (molecular != Atom::ATOMIC) {
              if (!moltemplate)
                which = find_special(special[i], nspecial[i], tag[j]);
              else if (imol >= 0)
                which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
                                     tag[j] - tagprev);
              else
                which = 0;
              if (which == 0)
                neighptr[n++] = j;
              else if (domain->minimum_image_check(delx, dely, delz))
                neighptr[n++] = j;
              else if (which > 0)
                neighptr[n++] = j ^ (which << SBBITS);
            } else
              neighptr[n++] = j;
          }
        }
      }
    }

    ilist[inum++] = i;
    firstneigh[i] = neighptr;
    numneigh[i] = n;
    ipage->vgot(n);
    if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
  }

  list->inum = inum;
  list->gnum = 0;
}

namespace LAMMPS_NS {
template class NPairMultiOld<0,1,0,0>;
template class NPairMultiOld<1,0,0,0>;
template class NPairMultiOld<1,1,0,0>;
template class NPairMultiOld<1,1,1,0>;
template class NPairMultiOld<0,1,0,1>;
template class NPairMultiOld<1,0,0,1>;
template class NPairMultiOld<1,1,0,1>;
template class NPairMultiOld<1,1,1,1>;
}